# [gmx-users] g_dipole ? =>salt-molecule => the relative position of counter ions to the rest of salt-molecule matters ???

Chih-Ying Lin chihying2008 at gmail.com
Thu Oct 21 21:20:04 CEST 2010

```HI

As Timo M.D. Graen described
"As long as the system is neutral, the reference point will not affect the
calculation result of the dipole moment for the system."

On the other hand, I also play around the small salt-molecule as Timo M.D.
Graen suggested.
"take two ions for a start, Na+ and Cl-, place
them at NA(1,1,0) and CL(2,1,0). Now calculate the dipole moment for
this system using different points of reference, i.e. (0,0,0) and
(1,2,0) and (3,3,0). What do you observe? Next, add an additional NA+
ion to your system at NA(3,1,0) and repeat your calculation for the same
reference points. "

So, i include the counter ion in my dipole moment-calculation this time.
But, the dipole moment of the system depends on where the counter ions are
located.
For the cis-structure, the dipole moment is range from 45 to 75 as I
randomly set the position of the counter ions.
For the trans-structure, the dipole is range from 35 to 77 as I randomly set
the position of the counter ions.

I have used GROMACS to test the dipole moment of the similar systems where
GROMACS set the positions of the counter ions and the rest of molecules.
For the cis-structure, the dipole moment is around 33.  The standard
deviation ~ 3
For the trans-structure, the dipole is around 36. The standard deviation ~ 3

How could GROMACS get the much lower standard deviation than what I
calculated?
Is there any specific rules while GROMACS decides the relative positions of
the counter ions to the rest of the molecules?
My calculation result is not very close to what GROMACS derived.
Am I doing correctly ?

For the cis-structure
Dipole moment from GROMACS
Average = 33.0312
Std. Dev. = 3.5144
Error = 0.0236
Dipole moment from my calculation = 45 to 75

For the trans-structure
Dipole moment from GROMACS
Average = 36.8470
Std. Dev. = 3.4917
Error = 0.0238
Dipole moment from my calculation = range from 35 to 77

Thank you
Lin

dipole moment = 48.0 sum of q_i x_i
x_i is the atomic position.

I did not include the counter ion of the salt molecule in my calculation.
The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans.
Here "A" are a string of atoms, most of them are carbons.

For the cis-structure
Dipole moment from GROMACS
Average = 33.0312
Std. Dev. = 3.5144
Error = 0.0236
Dipole moment from my calculation = 55.8675

For the trans-structure
Dipole moment from GROMACS
Average = 36.8470
Std. Dev. = 3.4917
Error = 0.0238
Dipole moment from my calculation = 77.2346

Questions:
1. There is a huge discrepancy between my calculation results and GROMACS.
Or, the two results are within acceptable discrepancy ???

2. In the beginning, I suppose that the trans-structure has smaller dipole
moment than cis-structure. However, it seems to be the opposite conclusion
based on both GROMACS and my calculation. Is there something possible wrong
???

3. I get the partial charges from the Journal papers and the partial charges
are derived for the similar molecules as mine. Is that wrong?

Thank you
Lin
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